This chapter provides a descriptive outline of the Bacteria, the Archaea, and some new chemical boundaries of their habitats in the more usual environmental sense (e.g., association with soils, waters, and some extreme environments) and also includes a consideration of microbes associated with macrobes. The recognition that beneath the widely disparate nutritional and environmental needs for the growth and sustenance of different microbes there was an underlying unity in their physiological attributes was a major conceptual contribution that had a marked practical influence on the development, nature, and extent of one's understanding of the significance of prokaryotic diversity. A widely accepted phylogenetic tree that classifies life in three major categories, Archaea, Bacteria, and Eucarya, is based on the inferences that Archaea and Eucarya diverged from ancestors of the Bacteria, first as a single lineage and only later diverging and becoming separately recognizable entities. As ever-increasing numbers of unique habitats are examined by use of macromolecular sequence, stable-isotope research, and new cultivation strategies, it is ever more evident that prokaryotic diversity has been regularly underestimated by classical isolation and cultivation approaches. Studies of Buchnera spp., the prokaryotic intracellular symbionts of aphids, are but one reminder that not all organisms of environmental significance are free-living and that some may exist in mutualistic states. With complete and accessible data collection, there is a good chance that even complex systems with multiple species may yield information that is comprehensible, leads to more accurate predictions, and may be used by the greater scientific community.

A phylogenetic tree based on evaluation of 16S rRNA sequences. The three major lineages of life (Archaea, Bacteria, and Eucarya) are shown. T. celer, Thermococcus celer. Reprinted from The FASEB Journal (99) with permission.

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FIGURE 1

A phylogenetic tree based on evaluation of 16S rRNA sequences. The three major lineages of life (Archaea, Bacteria, and Eucarya) are shown. T. celer, Thermococcus celer. Reprinted from The FASEB Journal (99) with permission.